Multivalent delivery of immune modulators by liposomal spherical nucleic acids for prophylactic or therapeutic applications

ABSTRACT

Liposomal spherical nucleic acids that function as multivalent immune modulators are provided according to the invention. The liposomal spherical nucleic acids of the invention are useful prophylactic and therapeutic applications as well as research and diagnostic indications.

RELATED APPLICATION

This application is a national stage filing under 35 U.S.C. § 371 of International Application No. PCT/US2015/034226, filed Jun. 4, 2015, which claims priority under 35 U.S.C. § 119(e) to U.S. Provisional Application Ser. No. 62/007,528, entitled “MULTIVALENT DELIVERY OF IMMUNE MODULATORS BY LIPOSOMAL SPHERICAL NUCLEIC ACIDS FOR PROPHYLACTIC OR THERAPEUTIC APPLICATIONS” filed on Jun. 4, 2014, which are herein incorporated by reference in their entireties.

NAMES OF PARTIES TO A JOINT RESEARCH AGREEMENT

The inventions disclosed herein were made pursuant to a joint research agreement between Exicure Inc. and Northwestern University.

BACKGROUND OF THE INVENTION

The immune system is a complex network of cellular and humoral components that act in concert to recognize foreign and potentially dangerous substances in the body and eliminate them in a highly targeted and controlled fashion. It can generally be divided into the innate and adaptive immune systems. The innate immune system is germline encoded and is designed to respond to conserved motifs present on pathogens. The adaptive immune system develops its antigen specificity repertoire through controlled somatic recombination processes and can respond with exquisite specificity to a wide variety of antigen types. Stimulating innate and adaptive immune responses have been shown to be an effective strategy to treat or prevent a wide variety of diseases in animals, animal disease models, and humans.

The success of immunomodulatory approaches in treating or preventing a variety of infectious diseases has been extraordinary. Despite this, there are potentially many more diseases that could be addressed using an immunotherapy approach. Two critical limitations remain: (1) properly priming innate immune cells with the right signals delivered at the optimal time and in optimal ratios to safely boost their function while also providing a suitable environment for inducing an adaptive immune response, and (2) identifying the right antigen or combination of antigens that should be targeted by the adaptive response.

Current approaches for stimulating an immune response largely depend on mixtures of compounds that are known to be immunomodulatory in isolation. At present, compounds that are used in the clinic are bulk mixtures of immune stimulants, optionally combined with antigens, which have been empirically determined to induce innate and adaptive immune responses, respectively. Despite almost a century of development, conventional approaches have yielded only two FDA approved immune stimulants: (1) alum, which is a combination of aluminum salts, and (2) monophosphoryl lipid A. While alum in particular has an impressive track record of safety and efficacy in infectious diseases, it is becoming increasingly clear that these agents do not appear sufficient to induce effective immune responses to combat more complex diseases, such as intracellular pathogens, cancer, allergies, and allergic diseases, among others. Efforts to develop new immunostimulants have largely been unsuccessful, primarily due to lack of efficacy or due to safety concerns.

The immune system evolved over millennia to respond to pathogens such as bacteria, viruses, fungi, and helminths. Consequently, most immune cells are optimized to recognize, phagocytose, process, and then respond to motifs present on microorganisms and have receptors that are “tuned” to the ratios typically present on these organisms.

SUMMARY OF THE INVENTION

Liposomal spherical nucleic acids that function as multivalent immune modulators are provided according to aspects of the invention. The invention is based, in some aspects, on a nanostructure, comprising a liposomal core having a lipid bilayer, wherein an immune stimulant or an immune suppressor is associated with the lipid bilayer, and oligonucleotides positioned on the exterior of the liposomal core.

In some embodiments the nanostructure comprises a liposomal core having a lipid bilayer, wherein an immune stimulant or an immune suppressor is associated with the lipid bilayer, and oligonucleotides positioned on the exterior of the liposomal core, wherein the oligonucleotides form an oligonucleotide shell.

In other embodiments the nanostructure comprises a liposomal core having a lipid bilayer, wherein an immune stimulant or an immune suppressor is associated with the lipid bilayer, and oligonucleotides positioned on the exterior of the liposomal core, wherein the oligonucleotides form an oligonucleotide shell, wherein the oligonucleotide shell is comprised of at least one pattern recognition receptor modulating oligonucleotide.

In some embodiments the nanostructure comprises a liposomal core having a lipid bilayer, wherein an immune stimulant or an immune suppressor is associated with the lipid bilayer, and oligonucleotides positioned on the exterior of the liposomal core, wherein the oligonucleotides form an oligonucleotide shell, wherein the oligonucleotide shell is comprised of at least one pattern recognition receptor modulating oligonucleotide, wherein the pattern recognition receptor modulating oligonucleotide is a TLR agonist.

In other embodiments the nanostructure comprises a liposomal core having a lipid bilayer, wherein an immune stimulant or an immune suppressor is associated with the lipid bilayer, and oligonucleotides positioned on the exterior of the liposomal core, wherein the oligonucleotides form an oligonucleotide shell, wherein the oligonucleotide shell is comprised of at least one pattern recognition receptor modulating oligonucleotide, wherein the pattern recognition receptor modulating oligonucleotide is a TLR antagonist.

In other embodiments the TLR is selected from the group consisting of TLR3, TLR 7, TLR8, TLR9, and TLR13.

In some embodiments the nanostructure comprises a liposomal core having a lipid bilayer, wherein an immune stimulant or an immune suppressor is associated with the lipid bilayer, and oligonucleotides positioned on the exterior of the liposomal core, wherein the oligonucleotides form an oligonucleotide shell, wherein the oligonucleotide shell is comprised of at least one pattern recognition receptor modulating oligonucleotide, wherein the pattern recognition receptor modulating oligonucleotide is a RIG-I agonist.

In other embodiments the nanostructure comprises a liposomal core having a lipid bilayer, wherein an immune stimulant or an immune suppressor is associated with the lipid bilayer, and oligonucleotides positioned on the exterior of the liposomal core, wherein the oligonucleotides form an oligonucleotide shell, wherein the oligonucleotide shell is comprised of at least one pattern recognition receptor modulating oligonucleotide, wherein the pattern recognition receptor modulating oligonucleotide is a RIG-I antagonist.

In some embodiments the oligonucleotide shell is comprised of oligonucleotides and a carrier molecule.

In other embodiments wherein the oligonucleotide shell is comprised entirely of oligonucleotides.

In some embodiments the oligonucleotides are comprised of single-stranded or double-stranded DNA oligonucleotides.

In other embodiments the oligonucleotides are comprised of single-stranded or double-stranded RNA oligonucleotides.

In other embodiments the oligonucleotides are comprised of chimeric RNA-DNA oligonucleotides.

In another embodiment the oligonucleotides are comprised of combinations of single-stranded or double-stranded DNA, RNA, or chimeric RNA-DNA oligonucleotides.

In another embodiment the oligonucleotides of the oligonucleotide shell have structurally identical oligonucleotides.

In some embodiments the oligonucleotides of the oligonucleotide shell have at least two structurally different oligonucleotides.

In other embodiments the oligonucleotides of the oligonucleotide shell have 2-10 different nucleotide sequences.

In some embodiments the oligonucleotides have at least one phosphorothioate linkage.

In other embodiments the oligonucleotides do not have a phosphorothioate linkage.

In another embodiment the nanostructure comprises a liposomal core having a lipid bilayer, wherein an immune stimulant or an immune suppressor is associated with the lipid bilayer, and oligonucleotides positioned on the exterior of the liposomal core, wherein the oligonucleotides comprise CpG-motif containing oligonucleotides.

In some embodiments the CpG oligonucleotides are selected from the group consisting of A-class, B-class and C-class CpG oligonucleotides.

In another embodiment the nanostructure comprises a liposomal core having a lipid bilayer, wherein an immune stimulant or an immune suppressor is associated with the lipid bilayer, and oligonucleotides positioned on the exterior of the liposomal core, wherein the oligonucleotides comprise immunostimulatory single-stranded or double-stranded RNA.

In some embodiments at least one oligonucleotide has its 5′-terminus exposed to the outside surface of the nanostructure.

In other embodiments all of the oligonucleotides have their 5′-terminus exposed to the outside surface of the nanostructure.

In another embodiment the oligonucleotides are directly linked to the liposomal core.

In some embodiments the oligonucleotides are indirectly linked to the liposomal core through a linker.

In other embodiments the oligonucleotides are indirectly linked to the liposomal core through more than one linker.

In another embodiment the linker is one or more of the following linkers: tocopherols, sphingolipids such as sphingosine, sphingosine phosphate, methylated sphingosines and sphinganines, ceramides, ceramide phosphates, 1-0 acyl ceramides, dihydroceramides, 2-hydroxy ceramides, sphingomyelin, glycosylated sphingolipids, sulfatides, gangliosides, phosphosphingolipids, and phytosphingosines of various lengths and saturation states and their derivatives, phospholipids such as phosphatidylcholines, lysophosphatidylcholines, phosphatidic acids, lysophosphatidic acids, cyclic LPA, phosphatidylethanolamines, lysophosphatidylethanolamines, phosphatidylglycerols, lysophosphatidylglycerols, phosphatidylserines, lysophosphatidylserines, phosphatidylinositols, inositol phosphates, LPI, cardiolipins, lysocardiolipins, bis(monoacylglycero) phosphates, (diacylglycero) phosphates, ether lipids, diphytanyl ether lipids, and plasmalogens of various lengths, saturation states, and their derivatives, sterols such as cholesterol, desmosterol, stigmasterol, lanosterol, lathosterol, diosgenin, sitosterol, zymosterol, zymostenol, 14-demethyl-lanosterol, cholesterol sulfate, DHEA, DHEA sulfate, 14-demethyl-14-dehydrlanosterol, sitostanol, campesterol, ether anionic lipids, ether cationic lipids, lanthanide chelating lipids, A-ring substituted oxysterols, B-ring substituted oxysterols, D-ring substituted oxysterols, side-chain substituted oxysterols, double substituted oxysterols, cholestanoic acid derivatives, fluorinated sterols, fluorescent sterols, sulfonated sterols, phosphorylated sterols, polyunsaturated sterols of different lengths, saturation states, saturated C8-C22 fatty acids, saturated C8-C22 ether derivatives of glycerol, saturated and unsaturated amide derivatives of C8-C22 fatty acids and mono- and 1,2- or 1, 3-di-amino glycerols and derivatives thereof.

In another embodiment the oligonucleotides comprise 2-1,000 oligonucleotides.

In some embodiments the liposomal core is comprised of one or more lipids selected from: sphingolipids such as sphingosine, sphingosine phosphate, methylated sphingosines and sphinganines, ceramides, ceramide phosphates, 1-0 acyl ceramides, dihydroceramides, 2-hydroxy ceramides, sphingomyelin, glycosylated sphingolipids, sulfatides, gangliosides, phosphosphingolipids, and phytosphingosines of various lengths and saturation states and their derivatives, phospholipids such as phosphatidylcholines, lysophosphatidylcholines, phosphatidic acids, lysophosphatidic acids, cyclic LPA, phosphatidylethanolamines, lysophosphatidylethanolamines, phosphatidylglycerols, lysophosphatidylglycerols, phosphatidylserines, lysophosphatidylserines, phosphatidylinositols, inositol phosphates, LPI, cardiolipins, lysocardiolipins, bis(monoacylglycero) phosphates, (diacylglycero) phosphates, ether lipids, diphytanyl ether lipids, and plasmalogens of various lengths, saturation states, and their derivatives, sterols such as cholesterol, desmosterol, stigmasterol, lanosterol, lathosterol, diosgenin, sitosterol, zymosterol, zymostenol, 14-demethyl-lanosterol, cholesterol sulfate, DHEA, DHEA sulfate, 14-demethyl-14-dehydrlanosterol, sitostanol, campesterol, ether anionic lipids, ether cationic lipids, lanthanide chelating lipids, A-ring substituted oxysterols, B-ring substituted oxysterols, D-ring substituted oxysterols, side-chain substituted oxysterols, double substituted oxysterols, cholestanoic acid derivatives, fluorinated sterols, fluorescent sterols, sulfonated sterols, phosphorylated sterols, and polyunsaturated sterols of different lengths, saturation states, saturated C8-C22 fatty acids, saturated C8-C22 ether derivatives of glycerol, and saturated and unsaturated amide derivatives of C8-C22 fatty acids and mono- and 1,2- or 1, 3-di-amino glycerols and derivatives thereof.

In another embodiment the liposomal core is comprised of one type of lipid.

In some embodiments the liposomal core is comprised of 2-10 different lipids.

In other embodiments wherein the immune stimulant is selected from the group consisting of monophosphoryl lipid A, lipid A from bacterial origin, 22:0 trehalose, dimethyldioctadecyl-ammonium, Kdo2 lipid A, inositol phosphates including IP3(1,3,4), IP3(1,3,5), IP3(1,4,5), IPR(1,3,4,5), LPA/S1P receptor selective agonists, PAF and PAF analogs, liponucleotides, cyclic LPA, bioactive ceramides, endocannabinoids, anandamides, lipid oxidation products, diacylglycerol phosphate, bacterial membrane lipids, N-acylglycine lipids, acyl carnitine lipids, mycolic acids, plant lipid extracts, FSL-1, PAM3CSK4, HKLM, LPS, FLA-ST, imiquimod, resiquimod, C12-IE-DAP, L18-MDP toll like receptor agonists, NOD receptor agonists, and pro-inflammatory immune receptor agonists.

In another embodiment the nanostructure further comprises an antigen.

In some embodiments the antigen is mixed together with the nanostructure.

In other embodiments the antigen is linked directly to the oligonucleotide shell.

In some embodiments the antigen is linked indirectly to the oligonucleotide shell through a linker.

In other embodiments the antigen is linked directly to the liposomal core.

In yet another embodiment the antigen is linked indirectly to the liposomal core through a linker.

In another embodiment wherein an antigen-oligonucleotide conjugate is linked to the liposomal core through oligonucleotide hybridization.

In some embodiments the nanostructure comprises a liposomal core having a lipid bilayer, wherein an immune stimulant or an immune suppressor is associated with the lipid bilayer, and oligonucleotides positioned on the exterior of the liposomal core, wherein the immune stimulant is associated with the liposomal core by being embedded within the liposomal core.

In other embodiments the nanostructure comprises a liposomal core having a lipid bilayer, wherein an immune stimulant or an immune suppressor is associated with the lipid bilayer, and oligonucleotides positioned on the exterior of the liposomal core, wherein the immune stimulant is associated with the liposomal core by being linked indirectly to the liposomal core.

In some embodiments the nanostructure comprises a liposomal core having a lipid bilayer, wherein an immune stimulant or an immune suppressor is associated with the lipid bilayer, and oligonucleotides positioned on the exterior of the liposomal core, wherein the immune stimulant is associated with the liposomal core by being linked directly to the liposomal core.

In some embodiments the nanostructure comprises a liposomal core having a lipid bilayer, wherein an immune stimulant or an immune suppressor is associated with the lipid bilayer, and oligonucleotides positioned on the exterior of the liposomal core, wherein the oligonucleotides form an oligonucleotide shell, wherein the oligonucleotides of the oligonucleotide shell are oriented radially outwards.

In other embodiments the linker is selected from the group consisting of tocopherols, sphingolipids such as sphingosine, sphingosine phosphate, methylated sphingosines and sphinganines, ceramides, ceramide phosphates, 1-0 acyl ceramides, dihydroceramides, 2-hydroxy ceramides, sphingomyelin, glycosylated sphingolipids, sulfatides, gangliosides, phosphosphingolipids, and phytosphingosines of various lengths and saturation states and their derivatives, phospholipids such as phosphatidylcholines, lysophosphatidylcholines, phosphatidic acids, lysophosphatidic acids, cyclic LPA, phosphatidylethanolamines, lysophosphatidylethanolamines, phosphatidylglycerols, lysophosphatidylglycerols, phosphatidylserines, lysophosphatidylserines, phosphatidylinositols, inositol phosphates, LPI, cardiolipins, lysocardiolipins, bis(monoacylglycero) phosphates, (diacylglycero) phosphates, ether lipids, diphytanyl ether lipids, and plasmalogens of various lengths, saturation states, and their derivatives, sterols such as cholesterol, desmosterol, stigmasterol, lanosterol, lathosterol, diosgenin, sitosterol, zymosterol, zymostenol, 14-demethyl-lanosterol, cholesterol sulfate, DHEA, DHEA sulfate, 14-demethyl-14-dehydrlanosterol, sitostanol, campesterol, ether anionic lipids, ether cationic lipids, lanthanide chelating lipids, A-ring substituted oxysterols, B-ring substituted oxysterols, D-ring substituted oxysterols, side-chain substituted oxysterols, double substituted oxysterols, cholestanoic acid derivatives, fluorinated sterols, fluorescent sterols, sulfonated sterols, phosphorylated sterols, and polyunsaturated sterols of different lengths, saturation states, saturated C8-C22 fatty acids, saturated C8-C22 ether derivatives of glycerol, saturated and unsaturated amide derivatives of C8-C22 fatty acids and mono- and 1,2- or 1, 3-di-amino glycerols, and derivatives thereof.

In some embodiments the antigen is encapsulated within the liposomal core in an inner aqueous layer.

In other embodiments the antigen is attached non-covalently to the oligonucleotide of the oligonucleotide shell.

In other embodiments the antigen is selected from the group consisting of a cancer antigen, a bacterial antigen, a viral antigen, a parasitic antigen, a hapten, and an allergen.

In some embodiments the nanostructure is a self-assembling nanostructure.

Another aspect of the invention comprises a method for treating a subject, comprising administering to a subject a nucleic acid nanostructure in an effective amount to promote an immune response.

In one embodiment the subject has a disorder and wherein the method is a method for treating the disorder.

In another embodiment the disorder is cancer.

In some embodiments the disorder is infectious disease.

In other embodiments the infectious disease is a viral infection.

In some embodiments the infectious disease is a bacterial infection.

In another embodiment the disorder is allergy.

In some embodiments the disorder is asthma.

In another embodiment the disorder is autoimmune disease.

In some embodiments further comprising administering a therapeutic protocol to the subject.

In another embodiment the therapeutic protocol is surgery.

In some embodiments the therapeutic protocol is radiation.

In other embodiments the therapeutic protocol is a medicament.

In one embodiment the method further comprises administering an adjuvant.

In one embodiment the subject has a disorder and wherein the method is a method for treating the disorder, wherein the nanostructure is associated with a targeting molecule.

In one embodiment the subject has a disorder and wherein the method is a method for treating the disorder, wherein the nanostructure is delivered by a route selected from the group consisting of oral, nasal, sublingual, intravenous, subcutaneous, mucosal, respiratory, direct injection, enema, and dermally.

In another aspect the composition for use in the treatment of disease comprises the nucleic acid nanostructure and embodiments thereof.

Each of the limitations of the invention can encompass various embodiments of the invention. It is, therefore, anticipated that each of the limitations of the invention involving any one element or combinations of elements can be included in each aspect of the invention. This invention is not limited in its application to the details of construction and the arrangement of components set forth in the following description or illustrated in the drawings. The invention is capable of other embodiments and of being practiced or of being carried out in various ways. The details of one or more embodiments of the invention are set forth in the accompanying Detailed Description, Examples, Claims, and Figures. Other features, objects, and advantages of the invention will be apparent from the description and from the claims.

BRIEF DESCRIPTION OF THE DRAWINGS

The accompanying drawings are not intended to be drawn to scale. In the drawings, each identical or nearly identical component that is illustrated in various figures is represented by a like numeral. For purposes of clarity, not every component may be labeled in every drawing. In the drawings:

FIG. 1 shows a general structure of an exemplary liposomal nanostructure of the invention for co-delivery of oligonucleotide and lipophilic immune stimulants. The nanostructure includes: (1) a liposomal core, which contains lipophilic immune stimulants (TLR1, TLR2, TLR4, TLR5, TLR6, among others) attached to and possibly embedded in the lipid bilayer, and (2) an oligonucleotide shell, which has dual function in that it helps to target the entire construct to immune cells and also acts to stimulate immune receptors that can recognize nucleic acids (TLR3, TLR7, TLR8, TLR9, TLR13, RIG-I, among others).

FIG. 2 shows a general structure of another exemplary antigen-conjugated liposomal nanostructure for co-delivery of oligonucleotide and lipophilic immune stimulants and antigen. The construct is similar to that shown in FIG. 1 but includes an additional modification whereby an antigen-conjugated oligonucleotide is attached non-covalently to the parent structure. The antigen is conjugated to the liposomal SNA via interactions with the oligonucleotide shell.

FIG. 3 shows another general structure of antigen-conjugated liposomal nanostructure for co-delivery of oligonucleotide and lipophilic immune stimulants and antigen. The antigen may also be encapsulated in the liposomal core.

FIG. 4 is a graph showing that stimulating both TLR4 and TLR9 via liposomal nanostructures induce greater activation than either in isolation. Liposomal nanostructures which carry agonists of both TLR4 and TLR9 induce greater activation of the RAW Blue cells than either alone in isolation.

FIGS. 5A-5B are a set of bar graphs showing that activation of NF-kB by MPLA is dependent on functional TLR4. Activation of NF-kB by liposomal SNAs containing MPLA depended on functional TLR4, as the RAW Blue cell line (FIG. 5A) but not the Ramos Blue cell line (FIG. 5B) demonstrated NF-kB activation in response to stimulation. One-way ANOVA ****p<0.0001, ***p<0.001, **p<0.01.

FIGS. 6A-6B are a set of bar graphs showing that nanostructure co-delivery of CpG and MPLA optimally activates both MyD88-dependent and -independent pathways. Liposomal nanostructures that deliver both CpG 1826 and MPLA in a single construct demonstrate elevated TNF (FIG. 6A) and IFN-alpha (FIG. 6B) levels that cannot be replicated either by delivering each in isolation, or by delivering both components in the same well but not on the same construct. ANOVA, **p<0.01, ****p<0.0001.

FIGS. 7A-7B are a set of bar graphs showing liposomal nanostructure delivery of MPLA improves activation of NF-kB even without CpG motif. FIG. 7A shows NF-kB activation and FIG. 7B shows TNF (OD). One-way ANOVA ****p<0.0001.

FIG. 8 is a graph showing that increasing MPLA feed into nanostructures formulation above 3.8% but not beyond 7.7% improves activity. In the RAW Blue cell line, it was observed that increasing the MPLA feed up to 7.7% MPLA but not up to 11.5% increased the potency of activation of the liposomal SNA.

FIG. 9 is a set of graphs showing that phosphorothioate (PS) linkages increase potency but not maximal stimulation in murine immune cells at 11.5% MPLA (top panel) or 7.7% MPLA (bottom panel). In the RAW Blue cells, a shift was observed in the potency of the liposomal nanostructures but not in the maximal stimulation, though this is anticipated to be species dependent.

FIG. 10 is a graph showing antigen-conjugated liposomal nanostructures demonstrates activation of immune cells.

FIG. 11 is a graph showing that nanostructures induce cellular responses more effectively than free PS oligo and alum. C57BL/6 mice (N=4/group) were immunized with the indicated formulations on day 0 and 21 using ovalbumin as the model antigen. On day 28, splenocytes were collected and incubated overnight on IFN-γ ELISPOT plates with 1 uM OVA(257-264). The number of IFN-γ spots was quantified using an automated ELISPOT counter. *p<0.05, NS=non-significant

FIG. 12 is a graph showing that hollow nanostructures with antigen reduce tumor growth rates. C57BL/6 mice (N=10/group) were inoculated with 1×10⁶ E.G7-OVA cells on day 0 then treated with the indicated compounds on days 3, 7, 10.

DETAILED DESCRIPTION OF CERTAIN EMBODIMENTS OF THE INVENTION

Toll-like receptors (TLRs) are a family of pattern recognition receptors (PRRs) that trigger activation of innate immune cells, promoting their effector functions and bridging innate and adaptive immunity. Agents that stimulate TLRs are being investigated extensively as potential therapeutic and prophylactic compounds due to the central role these receptors play in coordinating immune responses. Similar to the way that multiple TLRs and immune receptors are stimulated when an immune cell processes a pathogen, it has been shown that stimulation of multiple TLRs with multiple compounds can yield greater efficacy. However, effectively delivering multiple TLR agonists in combination can be quite difficult for a number of reasons: (1) synergy is often observed only in a narrow window of fixed concentration ratios between the two compounds, due to their typically different IC50 or EC50 values, (2) different physicochemical properties such as different size, charge, and hydrophobicity can make attaching them to each other difficult or make them have drastically different PK/PD/ADME properties, (3) the toxic levels of the compounds tend to be different, and (4) the target receptors of one or more of the different compounds may be inaccessible, such as the cytosol, or located in a degradative compartment, such as endosomes or lysosomes.

A novel class of nanostructures having unexpectedly high immune modulating activity have been developed according to the invention. These nanostructures are supra-molecular assemblies, which are immune-modulating liposomal spherical nucleic acids (sometimes referred to as SNAs). These nanostructures can deliver combinations of immune modulating materials in a highly spatiotemporally controlled manner to cells (Examples are shown in FIGS. 1-3). A distinctive feature of these nanostructures is the incorporation of immune modulating materials both within the external shell as well as within the core, which work in concert to achieve unexpected immune modulating effects in terms of the magnitude and quality of the immune response. These immunomodulating effects cannot be achieved by delivering the materials individually or in combination but not physically associated together in the same construct. It has been demonstrated according to the invention that the assembly of all components into a single structure is vital to achieving optimal effects (Data is shown in FIGS. 6-7).

In addition to the above, a method for achieving co-delivery of antigen with the multivalent immune-modulating structures was also developed (Examples are depicted in FIGS. 2-3). This enables these constructs to deliver both antigenic and co-stimulatory signals to bridge innate and adaptive immunity to induce robust immune responses against a variety of diseases (stimulatory application) or to elicit antigen-specific tolerance by delivering antigen in the absence of co-stimulation, achieved by lack of a stimulatory signal or by blocking immune signaling with antagonist molecules, leading to effector cell anergy or induction of regulatory T cells (regulatory application).

Currently, methods used in the clinic to induce immunologic effects generally fall into two categories: 1) compounds that activate or potentiate immune responses, such as vaccines and adjuvants, small molecule agonists of toll-like receptors such as imiquimod and resiquimod, or oligonucleotides such as ISS 1018 (Dynavax Technologies Corporation), among several others, and 2) compounds that act to reduce unwanted immune responses, such as corticosteroids, cyclosporine, and tacrolimus. These compounds have significant limitations known to those in the art.

In general, immune stimulation attempts in the prior art have been limited by a lack of ability to activate robust cellular immune responses to target antigen, leading to failures to develop efficacious and cost-effective vaccines for various infectious diseases, such as HIV, tuberculosis, malaria, dengue, chlamydia, and others. Similarly, various experimental vaccine compounds for cancer have failed to reach their primary end point in late stage clinical trials. A key challenge that does not yet appear to be satisfactorily met is a formulation of antigen and immune stimulant that can achieve superior results. The nanostructure of the invention achieved these goals, producing activation of strong cellular responses to antigen in vivo with evidence of significant (95%) reduction of tumor burden (FIG. 12).

The nanostructure of the invention include: (1) a liposomal core having a lipid bilayer, which contains an immune stimulant embedded in or attached to the lipid bilayer, and (2) a layer of oligonucleotides, which may be an oligonucleotide shell, and which have dual function in that they help to target the nanostructure to immune cells and also act to stimulate immune receptors that can recognize nucleic acids (FIG. 1). Antigen may also be coupled to this construct, such that it will be delivered together with the co-stimulatory signals (FIG. 2). A similar construct to that shown in FIG. 1 undergoes an additional modification whereby an antigen-conjugated oligonucleotide is attached to the nanostructure. Alternatively or additionally a water-soluble immune stimulant or antigen can be encapsulated in the core.

The nanostructure of the invention includes a liposomal core. A liposomal core as used herein refers to a centrally located core compartment formed by a component of the lipids or phospholipids that form a lipid bilayer. “Liposomes” are artificial, self closed vesicular structure of various sizes and structures, where one or several membranes encapsulate an aqueous core. Most typically liposome membranes are formed from lipid bilayers membranes, where the hydrophilic head groups are oriented towards the aqueous environment and the lipid chains are embedded in the lipophilic core. Liposomes can be formed as well from other amphiphilic monomeric and polymeric molecules, such as polymers, like block copolymers, or polypeptides. Unilamellar vesicles are liposomes defined by a single membrane enclosing an aqueous space. In contrast, oligo- or multilamellar vesicles are built up of several membranes. Typically, the membranes are roughly 4 nm thick and are composed of amphiphilic lipids, such as phospholipids, of natural or synthetic origin. Optionally, the membrane properties can be modified by the incorporation of other lipids such as sterols or cholic acid derivatives.

The lipid bilayer is composed of two layers of lipid molecules. Each lipid molecule in a layer is oriented substantially parallel to adjacent lipid bilayers, and two layers that form a bilayer have the polar ends of their molecules exposed to the aqueous phase and the non-polar ends adjacent to each other, as shown in the diagrams of FIGS. 1-3. The central aqueous region of the liposomal core may be empty or filled fully or partially with water, an aqueous emulsion, antigen, immune stimulant, immune suppressor or other therapeutic or diagnostic agent.

“Lipid” refers to its conventional sense as a generic term encompassing fats, lipids, alcohol-ether-soluble constituents of protoplasm, which are insoluble in water. Lipids usually consist of a hydrophilic and a hydrophobic moiety. In water lipids can self organize to form bilayers membranes, where the hydrophilic moieties (head groups) are oriented towards the aqueous phase, and the lipophilic moieties (acyl chains) are embedded in the bilayers core. Lipids can comprise as well two hydrophilic moieties (bola amphiphiles). In that case, membranes may be formed from a single lipid layer, and not a bilayer. Typical examples for lipids in the current context are fats, fatty oils, essential oils, waxes, steroid, sterols, phospholipids, glycolipids, sulpholipids, aminolipids, chromolipids, and fatty acids. The term encompasses both naturally occurring and synthetic lipids. Preferred lipids in connection with the present invention are: steroids and sterol, particularly cholesterol, phospholipids, including phosphatidyl, phosphatidylcholines and phosphatidylethanolamines and sphingomyelins. Where there are fatty acids, they could be about 12-24 carbon chains in length, containing up to 6 double bonds. The fatty acids are linked to the backbone, which may be derived from glycerol. The fatty acids within one lipid can be different (asymmetric), or there may be only 1 fatty acid chain present, e.g. lysolecithins. Mixed formulations are also possible, particularly when the non-cationic lipids are derived from natural sources, such as lecithins (phosphatidylcholines) purified from egg yolk, bovine heart, brain, liver or soybean.

The liposomal core can be constructed from one or more lipids known to those in the art including but not limited to: sphingolipids such as sphingosine, sphingosine phosphate, methylated sphingosines and sphinganines, ceramides, ceramide phosphates, 1-0 acyl ceramides, dihydroceramides, 2-hydroxy ceramides, sphingomyelin, glycosylated sphingolipids, sulfatides, gangliosides, phosphosphingolipids, and phytosphingosines of various lengths and saturation states and their derivatives, phospholipids such as phosphatidylcholines, lysophosphatidylcholines, phosphatidic acids, lysophosphatidic acids, cyclic LPA, phosphatidylethanolamines, lysophosphatidylethanolamines, phosphatidylglycerols, lysophosphatidylglycerols, phosphatidylserines, lysophosphatidylserines, phosphatidylinositols, inositol phosphates, LPI, cardiolipins, lysocardiolipins, bis(monoacylglycero) phosphates, (diacylglycero) phosphates, ether lipids, diphytanyl ether lipids, and plasmalogens of various lengths, saturation states, and their derivatives, sterols such as cholesterol, desmosterol, stigmasterol, lanosterol, lathosterol, diosgenin, sitosterol, zymosterol, zymostenol, 14-demethyl-lanosterol, cholesterol sulfate, DHEA, DHEA sulfate, 14-demethyl-14-dehydrlanosterol, sitostanol, campesterol, ether anionic lipids, ether cationic lipids, lanthanide chelating lipids, A-ring substituted oxysterols, B-ring substituted oxysterols, D-ring substituted oxysterols, side-chain substituted oxysterols, double substituted oxysterols, cholestanoic acid derivatives, fluorinated sterols, fluorescent sterols, sulfonated sterols, phosphorylated sterols, and polyunsaturated sterols of different lengths, saturation states, and their derivatives.

An immune stimulant is associated with the lipid bilayer of the liposomal core. An immune stimulant, as used herein, is a substance that causes stimulation of the immune system such that one or more immune factors, i.e., cytokines, immune cells, antibodies, chemokines are induced or activated. The immune response may comprise a cellular and/or a humoral response. The immune stimulant can be, for example, a small molecule, a nucleic acid, a protein, or a combination thereof. The immune stimulant may also be capable of activating expression of immune stimulatory molecules on cells of a localized microenvironment.

The immune stimulant incorporated into the bilayer can be a wide variety of molecules including but not limited to: monophosphoryl lipid A, lipid A from bacterial origin, 22:0 trehalose, dimethyldioctadecyl-ammonium, Kdo2 lipid A, inositol phosphates including IP3(1,3,4), IP3(1,3,5), IP3(1,4,5), IPR(1,3,4,5), LPA/S1P receptor selective agonists, PAF and PAF analogs, liponucleotides, cyclic LPA, bioactive ceramides, endocannabinoids, anandamides, lipid oxidation products, diacylglycerol phosphate, bacterial membrane lipids, N-acylglycine lipids, acyl carnitine lipids, mycolic acids, plant lipid extracts, FSL-1, PAM3CSK4, HKLM, LPS, FLA-ST, imiquimod, resiquimod, C12-IE-DAP, L18-MDP and other compounds known to those in the art that can stimulate toll like receptors, NOD receptors, and other pro-inflammatory immune receptors that would be productive towards inducing an immune response.

The immune stimulant is associated with the liposomal core. It may be associated with by being embedded within the core or it may be attached or linked, either indirectly (i.e. non-covalently or covalently through other molecules such a linkers) or directly (i.e. covalently).

The nanostructure of the invention also includes an oligonucleotide which is preferably a therapeutic oligonucleotide. An oligonucleotide, as used herein, refers to any nucleic acid containing molecule. The nucleic acid may be DNA, RNA, PNA, LNA, ENA or combinations or modifications thereof. It may also be single, double or triple stranded. A therapeutic oligonucleotide is an oligonucleotide that can function as a therapeutic and or diagnostic agent.

The oligonucleotides are positioned on the exterior of the liposomal core. At least one oligonucleotide is on the exterior. In some embodiments at least 25, 50, 75, 100, 200, 300, 400, 500, 600, 700, 800, 900 or 1,000 oligonucleotides or any range combination thereof are on the exterior of the liposomal core. In some embodiments, 1-1000, 10-500, 50-250, or 50-300 oligonucleotides are present on the surface. In some instance the oligonucleotides form an oligonucleotide shell. An oligonucleotide shell is formed when at least 50% of the available surface area of the exterior surface of the liposomal includes an oligonucleotide. In some embodiments at least 60%, 70%, 80%, 90%, 95%, 96%, 97% 98% or 99% of the available surface area of the exterior surface of the liposomal includes an oligonucleotide. The oligonucleotides of the oligonucleotide shell may be oriented in a variety of directions. In some embodiments the oligonucleotides are oriented radially outwards.

The oligonucleotides may be linked to the core or to one another and/or to other molecules such an antigens either directly or indirectly through a linker. The oligonucleotides may be conjugated to a linker via the 5′ end or the 3′ end. E.g. [Sequence, 5′-3′]-Linker or Linker-[Sequence, 5′-3′]. Some or all of the oligonucleotides of the nanostructure may be linked to one another either directly or indirectly through a covalent or non-covalent linkage. The linkage of one oligonucleotide to another oligonucleotide may be in addition to or alternatively to the linkage of that oligonucleotide to liposomal core. One or more of the oligonucleotides may also be linked to other molecules such as an antigen. The oligonucleotides may be linked to the antigen of the core either directly or indirectly through a covalent or non-covalent linkage.

The oligonucleotide shell can be a wide variety of molecules including but not limited to: single-stranded deoxyribonucleotides, ribonucleotides, and other single-stranded oligonucleotides incorporating one or a multiplicity of modifications known to those in the art, double-stranded deoxyribonucleotides, ribonucleotides, and other double-stranded oligonucleotides incorporating one or a multiplicity of modifications known to those in the art, oligonucleotide triplexes incorporating deoxyribonucleotides, ribonucleotides, or oligonucleotides that incorporate one or a multiplicity of modifications known to those in the art. In another embodiment one or a multiplicity of different oligonucleotides are present on the same surface of a single liposomal nanostructure.

The oligonucleotide shell may be anchored to the surface of the liposomal core through conjugation to one or a multiplicity of linker molecules including but not limited to: tocopherols, sphingolipids such as sphingosine, sphingosine phosphate, methylated sphingosines and sphinganines, ceramides, ceramide phosphates, 1-0 acyl ceramides, dihydroceramides, 2-hydroxy ceramides, sphingomyelin, glycosylated sphingolipids, sulfatides, gangliosides, phosphosphingolipids, and phytosphingosines of various lengths and saturation states and their derivatives, phospholipids such as phosphatidylcholines, lysophosphatidylcholines, phosphatidic acids, lysophosphatidic acids, cyclic LPA, phosphatidylethanolamines, lysophosphatidylethanolamines, phosphatidylglycerols, lysophosphatidylglycerols, phosphatidylserines, lysophosphatidylserines, phosphatidylinositols, inositol phosphates, LPI, cardiolipins, lysocardiolipins, bis(monoacylglycero) phosphates, (diacylglycero) phosphates, ether lipids, diphytanyl ether lipids, and plasmalogens of various lengths, saturation states, and their derivatives, sterols such as cholesterol, desmosterol, stigmasterol, lanosterol, lathosterol, diosgenin, sitosterol, zymosterol, zymostenol, 14-demethyl-lanosterol, cholesterol sulfate, DHEA, DHEA sulfate, 14-demethyl-14-dehydrlanosterol, sitostanol, campesterol, ether anionic lipids, ether cationic lipids, lanthanide chelating lipids, A-ring substituted oxysterols, B-ring substituted oxysterols, D-ring substituted oxysterols, side-chain substituted oxysterols, double substituted oxysterols, cholestanoic acid derivatives, fluorinated sterols, fluorescent sterols, sulfonated sterols, phosphorylated sterols, and polyunsaturated sterols of different lengths, saturation states, and their derivatives. The oligonucleotide may be a nucleic acid that interacts with a molecule or complex of molecules that when stimulated produce an immune response in response to that interaction. The molecule or complex of molecules may be a receptor. In some embodiments the oligonucleotide may be a pattern recognition receptor (PRR) modulating oligonucleotide. PRRs are a primitive part of the immune system composed of proteins expressed by cells of the innate immune system to identify pathogen-associated molecular patterns (PAMPs), which are associated with microbial pathogens or cellular stress, as well as damage-associated molecular patterns (DAMPs), which are associated with cell components released during cell damage. PRRs include but are not limited to membrane-bound PRRs, such as receptor kinases, toll-like receptors (TLR), and C-type lectin Receptors (CLR) (mannose receptors and asialoglycoprotein receptors); Cytoplasmic PRRs such as RIG-I-like receptors (RLR), RNA Helicases, Plant PRRs, and NonRD kinases; and secreted PRRs. PRR modulating oligonucleotides include but are not limited to TLR agonists, agonists or antagonists of RIG-I, transcription factors, cellular translation machinery, cellular transcription machinery, nucleic-acid acting enzymes, and nucleic acid associating autoantigens. One example of this embodiment is the use of unmethylated 5′-cytosine-phosphate-guanosine-3′ (CpG) motifs. Another is the use of 5′-UUG-3′ or 5′-UUA-3′ motifs. Still another is the use of long double stranded RNA.

A TLR agonist, as used herein is a nucleic acid molecule that interacts with and stimulates the activity of a TLR. Toll-like receptors (TLRs) are a family of highly conserved polypeptides that play a critical role in innate immunity in mammals. At least ten family members, designated TLR1-TLR10, have been identified. The cytoplasmic domains of the various TLRs are characterized by a Toll-interleukin 1 (IL-1) receptor (TIR) domain. Medzhitov R et al. (1998) Mol Cell 2:253-8. Recognition of microbial invasion by TLRs triggers activation of a signaling cascade that is evolutionarily conserved in Drosophila and mammals. The TIR domain-containing adaptor protein MyD88 has been reported to associate with TLRs and to recruit IL-1 receptor-associated kinase (IRAK) and tumor necrosis factor (TNF) receptor-associated factor 6 (TRAF6) to the TLRs. The MyD88-dependent signaling pathway is believed to lead to activation of NF-κB transcription factors and c-Jun NH₂ terminal kinase (Jnk) mitogen-activated protein kinases (MAPKs), critical steps in immune activation and production of inflammatory cytokines. For a review, see Aderem A et al. (2000) Nature 406:782-87.

TLRs are believed to be differentially expressed in various tissues and on various types of immune cells. For example, human TLR7 has been reported to be expressed in placenta, lung, spleen, lymph nodes, tonsil and on plasmacytoid precursor dendritic cells (pDCs). Chuang T-H et al. (2000) Eur Cytokine Netw 11:372-8); Kadowaki N et al. (2001) J Exp Med 194:863-9. Human TLR8 has been reported to be expressed in lung, peripheral blood leukocytes (PBL), placenta, spleen, lymph nodes, and on monocytes. Kadowaki N et al. (2001) J Exp Med 194:863-9; Chuang T-H et al. (2000) Eur Cytokine Netw 11:372-8. Human TLR9 is reportedly expressed in spleen, lymph nodes, bone marrow, PBL, and on pDCs, and B cells. Kadowaki N et al. (2001) J Exp Med 194:863-9; Bauer S et al. (2001) Proc Natl Acad Sci USA 98:9237-42; Chuang T-H et al. (2000) Eur Cytokine Netw 11:372-8.

Nucleotide and amino acid sequences of human and murine TLR7 are known. See, for example, GenBank Accession Nos. AF240467, AF245702, NM_016562, AF334942, NM_133211; and AAF60188, AAF78035, NP_057646, AAL73191, and AAL73192, the contents of all of which are incorporated herein by reference. Human TLR7 is reported to be 1049 amino acids long. Murine TLR7 is reported to be 1050 amino acids long. TLR7 polypeptides include an extracellular domain having a leucine-rich repeat region, a transmembrane domain, and an intracellular domain that includes a TIR domain.

Nucleotide and amino acid sequences of human and murine TLR8 are known. See, for example, GenBank Accession Nos. AF246971, AF245703, NM_016610, XM_045706, AY035890, NM_133212; and AAF64061, AAF78036, NP_057694, XP_045706, AAK62677, and NP_573475, the contents of all of which is incorporated herein by reference. Human TLR8 is reported to exist in at least two isoforms, one 1041 amino acids long and the other 1059 amino acids long. Murine TLR8 is 1032 amino acids long. TLR8 polypeptides include an extracellular domain having a leucine-rich repeat region, a transmembrane domain, and an intracellular domain that includes a TIR domain.

Nucleotide and amino acid sequences of human and murine TLR9 are known. See, for example, GenBank Accession Nos. NM_017442, AF259262, AB045180, AF245704, AB045181, AF348140, AF314224, NM_031178; and NP_059138, AAF72189, BAB19259, AAF78037, BAB19260, AAK29625, AAK28488, and NP_112455, the contents of all of which are incorporated herein by reference. Human TLR9 is reported to exist in at least two isoforms, one 1032 amino acids long and the other 1055 amino acids. Murine TLR9 is 1032 amino acids long. TLR9 polypeptides include an extracellular domain having a leucine-rich repeat region, a transmembrane domain, and an intracellular domain that includes a TIR domain.

As used herein, the term “TLR signaling” refers to any aspect of intracellular signaling associated with signaling through a TLR. As used herein, the term “TLR-mediated immune response” refers to the immune response that is associated with TLR signaling. The level of TLR signaling may be enhanced over a pre-existing level of signaling or it may be induced over a background level of signaling.

A TLR3-mediated immune response is a response associated with TLR3 signaling. TLR3 agonists include but are not limited to dsRNA such as dsRNA having multiple AU motifs.

A TLR7-mediated immune response is a response associated with TLR7 signaling. TLR7-mediated immune response is generally characterized by the induction of IFN-α and IFN-inducible cytokines such as IP-10 and I-TAC. The levels of cytokines IL-1 α/β, IL-6, IL-8, MIP-1α/β and MIP-3α/β induced in a TLR7-mediated immune response are less than those induced in a TLR8-mediated immune response. TLR7 ligands include, without limitation, guanosine analogues such as C8-substituted guanosines, mixtures of ribonucleosides consisting essentially of G and U, guanosine ribonucleotides and RNA or RNA-like molecules (PCT/US03/10406), and adenosine-based compounds (e.g., 6-amino-9-benzyl-2-(3-hydroxy-propoxy)-9H-purin-8-ol, and similar compounds made by Sumitomo (e.g., CL-029)).

As used herein, the term “guanosine analogues” refers to a guanosine-like nucleotide (excluding guanosine) having a chemical modification involving the guanine base, guanosine nucleoside sugar, or both the guanine base and the guanosine nucleoside sugar. Guanosine analogues specifically include, without limitation, 7-deaza-guanosine.

Guanosine analogues further include C8-substituted guanosines such as 7-thia-8-oxoguanosine (immunosine), 8-mercaptoguanosine, 8-bromoguanosine, 8-methylguanosine, 8-oxo-7,8-dihydroguanosine, C8-arylamino-2′-deoxyguanosine, C8-propynyl-guanosine, C8- and N7-substituted guanine ribonucleosides such as 7-allyl-8-oxoguanosine (loxoribine) and 7-methyl-8-oxoguanosine, 8-aminoguanosine, 8-hydroxy-2′-deoxyguanosine, 8-hydroxyguanosine, and 7-deaza 8-substituted guanosine.

A TLR8-mediated immune response is a response associated with TLR8 signaling. This response is further characterized by the induction of pro-inflammatory cytokines such as IFN-γ, IL-12p40/70, TNF-α, IL-1α/β, IL-6, IL-8, MIP-1 α/β and MIP-3 α/β. TLR8 ligands include mixtures of ribonucleosides consisting essentially of G and U, guanosine ribonucleotides and RNA or RNA-like molecules (PCT/US03/10406). Additional TLR8 ligands are also disclosed in Gorden et al. J. Immunol. 2005, 174:1259-1268).

As used herein, a “TLR7/8 agonist” collectively refers to any nucleic acid that is capable of increasing TLR7 and/or TLR8 signaling (i.e., an agonist of TLR7 and/or TLR8). Some TLR7/8 ligands induce TLR7 signaling alone (e.g., TLR7 specific agonists), some induce TLR8 signaling alone (e.g., TLR8 specific agonists), and others induce both TLR7 and TLR8 signaling.

A TLR9-mediated immune response is a response associated with TLR9 signaling. This response is further characterized at least by the production/secretion of IFN-γ and IL-12, albeit at levels lower than are achieved via a TLR8-mediated immune response. As used herein, the term “TLR9 agonist” refers to any agent that is capable of increasing TLR9 signaling (i.e., an agonist of TLR9). TLR9 agonists specifically include, without limitation, immunostimulatory nucleic acids, and in particular CpG immunostimulatory nucleic acids.

“Immunostimulatory CpG nucleic acids” or “immunostimulatory CpG oligonucleotides” refers to any CpG-containing nucleic acid that is capable of activating an immune cell. At least the C of the CpG dinucleotide is typically, but not necessarily, unmethylated. Immunostimulatory CpG nucleic acids are described in a number of issued patents and published patent applications, including U.S. Pat. Nos. 6,194,388; 6,207,646; 6,218,371; 6,239,116; 6,339,068; 6,406,705; and 6,429,199.

A TLR13-mediated immune response is a response associated with TLR13 signaling. A TLR13 agonist is bacterial 23S rRNA.

The oligonucleotides may also be retinoic acid inducible gene-I (RIG-I) agonists or antagonists. RIG-I corresponds to GenBank Accession No. AF038963. RIG-I agonists include but are not limited to dsRNA such as Poly(I:C). RIG-I antagonists include short 5′ triphosphate DNA or RNA.

An “immunostimulatory oligonucleotide” is any nucleic acid (DNA or RNA) containing an immunostimulatory motif or backbone that is capable of inducing an immune response. An induction of an immune response refers to any increase in number or activity of an immune cell, or an increase in expression or absolute levels of an immune factor, such as a cytokine. Immune cells include, but are not limited to, NK cells, CD4+ T lymphocytes, CD8+ T lymphocytes, B cells, dendritic cells, macrophage and other antigen-presenting cells. Cytokines include, but are not limited to, interleukins, TNF-α, IFN-α,β and γ, Flt-ligand, and co-stimulatory molecules. Immunostimulatory motifs include, but are not limited to CpG motifs and T-rich motifs.

A non-limiting set of immunostimulatory oligonucleotides includes:

dsRNA:

poly(A:C) and poly(I:C)

ssRNA:

(SEQ ID NO: 4) CCGUCUGUUGUGUGACUC (SEQ ID NO: 6) GCCACCGAGCCGAAGGCACC (SEQ ID NO: 7) UAUAUAUAUAUAUAUAUAUA (SEQ ID NO: 8) UUAUUAUUAUUAUUAUUAUU (SEQ ID NO: 9) UUUUAUUUUAUUUUAUUUUA (SEQ ID NO: 10) UGUGUGUGUGUGUGUGUGUG  (SEQ ID NO: 11) UUGUUGUUGUUGUUGUUGUU (SEQ ID NO: 12) UUUGUUUGUUUGUUUGUUUG (SEQ ID NO: 13) UUAUUUAUUUAUUUAUUUAUUUAU (SEQ ID NO: 14) UUGUUUGUUUGUUUGUUUGUUUGU (SEQ ID NO: 15) GCCCGUCUGUUGUGUGACUC (SEQ ID NO: 16) GUCCUUCAAGUCCUUCAA

DNA:

(SEQ ID NO: 5) GGTGCATCGATGCAGGGGGG (SEQ ID NO: 17) TCCATGGACGTTCCTGAGCGTT (SEQ ID NO: 18) TCGTCGTTCGAACGACGTTGAT (SEQ ID NO: 19) TCGTCGACGATCCGCGCGCGCG (SEQ ID NO: 20) GGGGTCAACGTTGAGGGGGG (SEQ ID NO: 21) TCGTCGTTTTGTCGTTTTGTCGTT (SEQ ID NO: 22) TCGTCGTTGTCGTTTTGTCGTT (SEQ ID NO: 23) GGGGGACGATCGTCGGGGGG (SEQ ID NO: 24) GGGGACGACGTCGTGGGGGGG (SEQ ID NO: 25) TCGTCGTTTTCGGCGCGCGCCG (SEQ ID NO: 26) TCGTCGTCGTTCGAACGACGTTGAT

The terms “oligonucleotide” and “nucleic acid” are used interchangeably to mean multiple nucleotides (i.e., molecules comprising a sugar (e.g., ribose or deoxyribose) linked to a phosphate group and to an exchangeable organic base, which is either a substituted pyrimidine (e.g., cytosine (C), thymidine (T) or uracil (U)) or a substituted purine (e.g., adenine (A) or guanine (G)). Thus, the term embraces both DNA and RNA oligonucleotides. The terms shall also include oligonucleosides (i.e., a oligonucleotide minus the phosphate) and any other organic base containing polymer. Oligonucleotides can be obtained from existing nucleic acid sources (e.g., genomic or cDNA), but are preferably synthetic (e.g., produced by nucleic acid synthesis).

The oligonucleotides may be single stranded or double stranded. A double stranded oligonucleotide is also referred to herein as a duplex. Double-stranded oligonucleotides of the invention can comprise two separate complementary nucleic acid strands.

As used herein, “duplex” includes a double-stranded nucleic acid molecule(s) in which complementary sequences or partially complementary sequences are hydrogen bonded to each other. The complementary sequences can include a sense strand and an antisense strand. The antisense nucleotide sequence can be identical or sufficiently identical to the target gene to mediate effective target gene inhibition (e.g., at least about 98% identical, 96% identical, 94%, 90% identical, 85% identical, or 80% identical) to the target gene sequence.

A double-stranded oligonucleotide can be double-stranded over its entire length, meaning it has no overhanging single-stranded sequences and is thus blunt-ended. In other embodiments, the two strands of the double-stranded oligonucleotide can have different lengths producing one or more single-stranded overhangs. A double-stranded oligonucleotide of the invention can contain mismatches and/or loops or bulges. In some embodiments, it is double-stranded over at least about 70%, 80%, 90%, 95%, 96%, 97%, 98% or 99% of the length of the oligonucleotide. In some embodiments, the double-stranded oligonucleotide of the invention contains at least or up to 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, or 15 mismatches.

Oligonucleotides associated with the invention can be modified such as at the sugar moiety, the phosphodiester linkage, and/or the base. As used herein, “sugar moieties” includes natural, unmodified sugars, including pentose, ribose and deoxyribose, modified sugars and sugar analogs. Modifications of sugar moieties can include replacement of a hydroxyl group with a halogen, a heteroatom, or an aliphatic group, and can include functionalization of the hydroxyl group as, for example, an ether, amine or thiol.

Modification of sugar moieties can include 2′-O-methyl nucleotides, which are referred to as “methylated.” In some instances, oligonucleotides associated with the invention may only contain modified or unmodified sugar moieties, while in other instances, oligonucleotides contain some sugar moieties that are modified and some that are not.

In some instances, modified nucleomonomers include sugar- or backbone-modified ribonucleotides. Modified ribonucleotides can contain a non-naturally occurring base such as uridines or cytidines modified at the 5′-position, e.g., 5′-(2-amino)propyl uridine and 5′-bromo uridine; adenosines and guanosines modified at the 8-position, e.g., 8-bromo guanosine; deaza nucleotides, e.g., 7-deaza-adenosine; and N-alkylated nucleotides, e.g., N6-methyl adenosine. Also, sugar-modified ribonucleotides can have the 2′-OH group replaced by an H, alkoxy (or OR), R or alkyl, halogen, SH, SR, amino (such as NH₂, NHR, NR₂), or CN group, wherein R is lower alkyl, alkenyl, or alkynyl. In some embodiments, modified ribonucleotides can have the phosphodiester group connecting to adjacent ribonucleotides replaced by a modified group, such as a phosphorothioate group.

In some aspects, 2′-O-methyl modifications can be beneficial for reducing undesirable cellular stress responses, such as the interferon response to double-stranded nucleic acids. Modified sugars can include D-ribose, 2′-O-alkyl (including 2′-O-methyl and 2′-O-ethyl), i.e., 2′-alkoxy, 2′-amino, 2′-S-alkyl, 2′-halo (including 2′-fluoro), 2′-methoxyethoxy, 2′-allyloxy (—OCH₂CH═CH₂), 2′-propargyl, 2′-propyl, ethynyl, ethenyl, propenyl, and cyano and the like. The sugar moiety can also be a hexose.

The term “alkyl” includes saturated aliphatic groups, including straight-chain alkyl groups (e.g., methyl, ethyl, propyl, butyl, pentyl, hexyl, heptyl, octyl, nonyl, decyl, etc.), branched-chain alkyl groups (isopropyl, tert-butyl, isobutyl, etc.), cycloalkyl (alicyclic) groups (cyclopropyl, cyclopentyl, cyclohexyl, cycloheptyl, cyclooctyl), alkyl substituted cycloalkyl groups, and cycloalkyl substituted alkyl groups. In some embodiments, a straight chain or branched chain alkyl has 6 or fewer carbon atoms in its backbone (e.g., C₁-C₆ for straight chain, C₃-C₆ for branched chain), and more preferably 4 or fewer. Likewise, preferred cycloalkyls have from 3-8 carbon atoms in their ring structure, and more preferably have 5 or 6 carbons in the ring structure. The term C₁-C₆ includes alkyl groups containing 1 to 6 carbon atoms.

Unless otherwise specified, the term alkyl includes both “unsubstituted alkyls” and “substituted alkyls,” the latter of which refers to alkyl moieties having independently selected substituents replacing a hydrogen on one or more carbons of the hydrocarbon backbone. The term “alkenyl” includes unsaturated aliphatic groups analogous in length and possible substitution to the alkyls described above, but that contain at least one double bond. Unless otherwise specified, the term alkenyl includes both “unsubstituted alkenyls” and “substituted alkenyls,” the latter of which refers to alkenyl moieties having independently selected substituents replacing a hydrogen on one or more carbons of the hydrocarbon backbone.

The term “base” includes the known purine and pyrimidine heterocyclic bases, deazapurines, and analogs (including heterocyclic substituted analogs, e.g., aminoethyoxy phenoxazine), derivatives (e.g., 1-alkyl-, 1-alkenyl-, heteroaromatic- and 1-alkynyl derivatives) and tautomers thereof. Examples of purines include adenine, guanine, inosine, diaminopurine, and xanthine and analogs (e.g., 8-oxo-N⁶-methyladenine or 7-diazaxanthine) and derivatives thereof. Pyrimidines include, for example, thymine, uracil, and cytosine, and their analogs (e.g., 5-methylcytosine, 5-methyluracil, 5-(1-propynyl)uracil, 5-(1-propynyl)cytosine and 4,4-ethanocytosine). Other examples of suitable bases include non-purinyl and non-pyrimidinyl bases such as 2-aminopyridine and triazines.

In some aspects, the nucleomonomers of a oligonucleotide of the invention are RNA nucleotides, including modified RNA nucleotides.

The term “nucleoside” includes bases which are covalently attached to a sugar moiety, preferably ribose or deoxyribose. Examples of preferred nucleosides include ribonucleosides and deoxyribonucleosides. Nucleosides also include bases linked to amino acids or amino acid analogs which may comprise free carboxyl groups, free amino groups, or protecting groups. Suitable protecting groups are well known in the art (see P. G. M. Wuts and T. W. Greene, “Protective Groups in Organic Synthesis”, 2^(nd) Ed., Wiley-Interscience, New York, 1999).

As used herein, the term “linkage” used in the context of an internucleotide linkage includes a naturally occurring, unmodified phosphodiester moiety (—O—(PO²⁻)—O—) that covalently couples adjacent nucleomonomers. As used herein, the term “substitute linkage” or “modified linkage” or modified internucleotide linkage” includes any analog or derivative of the native phosphodiester group that covalently couples adjacent nucleomonomers.

Substitute linkages include phosphodiester analogs, e.g., phosphorothioate, phosphorodithioate, and P-ethyoxyphosphodiester, P-ethoxyphosphodiester, P-alkyloxyphosphotriester, methylphosphonate, and nonphosphorus containing linkages, e.g., acetals and amides. Such substitute linkages are known in the art (e.g., Bjergarde et al. 1991. Nucleic Acids Res. 19:5843; Caruthers et al. 1991. Nucleosides Nucleotides. 10:47). In certain embodiments, non-hydrolizable linkages are preferred, such as phosphorothioate linkages.

In some aspects, oligonucleotides of the invention comprise 3′ and 5′ termini (except for circular oligonucleotides). The 3′ and 5′ termini of a oligonucleotide can be substantially protected from nucleases, for example, by modifying the 3′ or 5′ linkages (e.g., U.S. Pat. No. 5,849,902 and WO 98/13526). Oligonucleotides can be made resistant by the inclusion of a “blocking group.” The term “blocking group” as used herein refers to substituents (e.g., other than OH groups) that can be attached to oligonucleotides or nucleomonomers, either as protecting groups or coupling groups for synthesis (e.g., FITC, propyl (CH₂—CH₂—CH₃), glycol (—O—CH₂—CH₂—O—) phosphate (PO₃ ²⁻), hydrogen phosphonate, or phosphoramidite). “Blocking groups” also include “end blocking groups” or “exonuclease blocking groups” which protect the 5′ and 3′ termini of the oligonucleotide, including modified nucleotides and non-nucleotide exonuclease resistant structures.

Exemplary end-blocking groups include cap structures (e.g., a 7-methylguanosine cap), inverted nucleomonomers, e.g., with 3′-3′ or 5′-5′ end inversions (see, e.g., Ortiagao et al. 1992. Antisense Res. Dev. 2:129), methylphosphonate, phosphoramidite, non-nucleotide groups (e.g., non-nucleotide linkers, amino linkers, conjugates) and the like. The 3′ terminal nucleomonomer can comprise a modified sugar moiety. The 3′ terminal nucleomonomer comprises a 3′-O that can optionally be substituted by a blocking group that prevents 3′-exonuclease degradation of the oligonucleotide. For example, the 3′-hydroxyl can be esterified to a nucleotide through a 3′→3′ internucleotide linkage. For example, the alkyloxy radical can be methoxy, ethoxy, or isopropoxy, and preferably, ethoxy. Optionally, the 3′→3′ linked nucleotide at the 3′ terminus can be linked by a substitute linkage. To reduce nuclease degradation, the 5′ most 3′→5′ linkage can be a modified linkage, e.g., a phosphorothioate or a P-alkyloxyphosphotriester linkage. Preferably, the two 5′ most 3′→5′ linkages are modified linkages. Optionally, the 5′ terminal hydroxy moiety can be esterified with a phosphorus containing moiety, e.g., phosphate, phosphorothioate, or P-ethoxyphosphate.

In some aspects, oligonucleotides can be chimeric RNA-DNA oligonucleotides which include both DNA and RNA.

The oligonucleotides are preferably in the range of 6 to 100 bases in length. However, nucleic acids of any size greater than 4 nucleotides (even many kb long) are capable of inducing a biological response according to the invention if sufficient stimulatory motifs are present. Preferably the nucleic acid is in the range of between 8 and 100 and in some embodiments between 8 and 50 or 8 and 30 nucleotides in size.

In some embodiments the oligonucleotides have a modified backbone such as a phosphorothioate (PS) backbone. In other embodiments the oligonucleotides have a phosphodiester (PO) backbone. In yet other embodiments oligonucleotides have a mixed or chimeric PO and PS backbone.

The nanostructure may also include an antigen. An antigen as used herein is a molecule capable of provoking an immune response in the body, especially the production of antibodies. Antigens include but are not limited to cells, cell extracts, proteins, polypeptides, peptides, polysaccharides, polysaccharide conjugates, peptide and non-peptide mimics of polysaccharides and other molecules, small molecules, lipids, glycolipids, carbohydrates, viruses and viral extracts and multicellular organisms such as parasites and allergens. The term antigen broadly includes any type of molecule which is recognized by a host immune system as being foreign. Antigens include but are not limited to cancer antigens, microbial antigens, and allergens.

Antigen can be attached to the structures by the externally-facing oligonucleotide through covalent or non-covalent, e.g. Watson/Crick hybridization. Alternatively or additionally the antigen may be incorporated into the liposomal bilayer via conjugation to a hydrophobic moiety (FIGS. 2-3). The data presented herein demonstrates that this form of antigen delivery provokes unexpectedly more potent induction of immune stimulatory effects in vitro (FIG. 10) and induces effective antigen processing and presentation, leading to effective induction of an anti-tumor immune response in vivo at highly unexpected levels (FIG. 11-12). In yet another embodiment, antigen may be incorporated inside the inner aqueous layer of the liposome (FIG. 3).

In one embodiment, antigen is conjugated to the liposomal nanostructure via interactions with the oligonucleotide shell (FIG. 2). In some instances the antigen-oligonucleotide conjugate is linked to the liposomal core through oligonucleotide hybridization. In other words the oligonucleotide is hybridized to a complementary or partially complementary oligonucleotide to form a duplex or partial duplex. One or both of the oligonucleotides of the duplex is linked directly to the liposomal core and the antigen which is external facing (on the outside of the lipid bilayer) or which is internal (in the inner aqueous layer) and not directly linked to the liposomal core is linked to one or both of the oligonucleotides in the duplex. In another embodiment, antigen is conjugated to the liposomal nanostructure via direct interactions with the liposomal core (FIG. 3). The antigen can be anchored to the surface of the liposomal core through conjugation to one or a multiplicity of linker molecules including but not limited to: tocopherols, sphingolipids such as sphingosine, sphingosine phosphate, methylated sphingosines and sphinganines, ceramides, ceramide phosphates, 1-0 acyl ceramides, dihydroceramides, 2-hydroxy ceramides, sphingomyelin, glycosylated sphingolipids, sulfatides, gangliosides, phosphosphingolipids, and phytosphingosines of various lengths and saturation states and their derivatives, phospholipids such as phosphatidylcholines, lysophosphatidylcholines, phosphatidic acids, lysophosphatidic acids, cyclic LPA, phosphatidylethanolamines, lysophosphatidylethanolamines, phosphatidylglycerols, lysophosphatidylglycerols, phosphatidylserines, lysophosphatidylserines, phosphatidylinositols, inositol phosphates, LPI, cardiolipins, lysocardiolipins, bis(monoacylglycero) phosphates, (diacylglycero) phosphates, ether lipids, diphytanyl ether lipids, and plasmalogens of various lengths, saturation states, and their derivatives, sterols such as cholesterol, desmosterol, stigmasterol, lanosterol, lathosterol, diosgenin, sitosterol, zymosterol, zymostenol, 14-demethyl-lanosterol, cholesterol sulfate, DHEA, DHEA sulfate, 14-demethyl-14-dehydrlanosterol, sitostanol, campesterol, ether anionic lipids, ether cationic lipids, lanthanide chelating lipids, A-ring substituted oxysterols, B-ring substituted oxysterols, D-ring substituted oxysterols, side-chain substituted oxysterols, double substituted oxysterols, cholestanoic acid derivatives, fluorinated sterols, fluorescent sterols, sulfonated sterols, phosphorylated sterols, and polyunsaturated sterols of different lengths, saturation states, and their derivatives.

A cancer antigen as used herein is a compound, such as a peptide or protein, associated with a tumor or cancer cell surface and which is capable of provoking an immune response when expressed on the surface of an antigen presenting cell in the context of an MHC molecule. Cancer antigens can be prepared from cancer cells either by preparing crude extracts of cancer cells, for example, as described in Cohen, et al., 1994, Cancer Research, 54:1055, by partially purifying the antigens, by recombinant technology, or by de novo synthesis of known antigens. Cancer antigens include but are not limited to antigens that are recombinantly expressed, an immunogenic portion of, or a whole tumor or cancer. Such antigens can be isolated or prepared recombinantly or by any other means known in the art.

A microbial antigen as used herein is an antigen of a microorganism and includes but is not limited to virus, bacteria, parasites, and fungi. Such antigens include the intact microorganism as well as natural isolates and fragments or derivatives thereof and also synthetic compounds which are identical to or similar to natural microorganism antigens and induce an immune response specific for that microorganism. A compound is similar to a natural microorganism antigen if it induces an immune response (humoral and/or cellular) to a natural microorganism antigen. Such antigens are used routinely in the art and are well known to those of ordinary skill in the art.

Examples of viruses that have been found in humans include but are not limited to: Retroviridae (e.g. human immunodeficiency viruses, such as HIV-1 (also referred to as HDTV-III, LAVE or HTLV-III/LAV, or HIV-III; and other isolates, such as HIV-LP; Picornaviridae (e.g. polio viruses, hepatitis A virus; enteroviruses, human Coxsackie viruses, rhinoviruses, echoviruses); Calciviridae (e.g. strains that cause gastroenteritis); Togaviridae (e.g. equine encephalitis viruses, rubella viruses); Flaviridae (e.g. dengue viruses, encephalitis viruses, yellow fever viruses); Coronoviridae (e.g. coronaviruses); Rhabdoviradae (e.g. vesicular stomatitis viruses, rabies viruses); Filoviridae (e.g. ebola viruses); Paramyxoviridae (e.g. parainfluenza viruses, mumps virus, measles virus, respiratory syncytial virus); Orthomyxoviridae (e.g. influenza viruses); Bungaviridae (e.g. Hantaan viruses, bunga viruses, phleboviruses and Nairo viruses); Arena viridae (hemorrhagic fever viruses); Reoviridae (e.g. reoviruses, orbiviurses and rotaviruses); Birnaviridae; Hepadnaviridae (Hepatitis B virus); Parvovirida (parvoviruses); Papovaviridae (papilloma viruses, polyoma viruses); Adenoviridae (most adenoviruses); Herpesviridae (herpes simplex virus (HSV) 1 and 2, varicella zoster virus, cytomegalovirus (CMV), herpes virus; Poxviridae (variola viruses, vaccinia viruses, pox viruses); and Iridoviridae (e.g. African swine fever virus); and other viruses (e.g. the agent of delta hepatitis (thought to be a defective satellite of hepatitis B virus), Hepatitis C; Norwalk and related viruses, and astroviruses).

Both gram negative and gram positive bacteria serve as antigens in vertebrate animals. Such gram positive bacteria include, but are not limited to, Pasteurella species, Staphylococci species, and Streptococcus species. Gram negative bacteria include, but are not limited to, Escherichia coli, Pseudomonas species, and Salmonella species. Specific examples of infectious bacteria include but are not limited to, Helicobacter pyloris, Borelia burgdorferi, Legionella pneumophilia, Mycobacteria sps (e.g. M. tuberculosis, M. avium, M. intracellulare, M. kansaii, M. gordonae), Staphylococcus aureus, Neisseria gonorrhoeae, Neisseria meningitidis, Listeria monocytogenes, Streptococcus pyogenes (Group A Streptococcus), Streptococcus agalactiae (Group B Streptococcus), Streptococcus (viridans group), Streptococcus faecalis, Streptococcus bovis, Streptococcus (anaerobic sps.), Streptococcus pneumoniae, pathogenic Campylobacter sp., Enterococcus sp., Haemophilus influenzae, Bacillus antracis, corynebacterium diphtheriae, corynebacterium sp., Erysipelothrix rhusiopathiae, Clostridium perfringers, Clostridium tetani, Enterobacter aerogenes, Klebsiella pneumoniae, Pasteurella multocida, Bacteroides sp., Fusobacterium nucleatum, Streptobacillus moniliformis, Treponema pallidium, Treponema pertenue, Leptospira, Rickettsia, and Actinomyces israelli.

Examples of fungi include Cryptococcus neoformans, Histoplasma capsulatum, Coccidioides immitis, Blastomyces dermatitidis, Chlamydia trachomatis, Candida albicans.

Other infectious organisms (i.e., protists) include Plasmodium spp. such as Plasmodium falciparum, Plasmodium malariae, Plasmodium ovale, and Plasmodium vivax and Toxoplasma gondii. Blood-borne and/or tissues parasites include Plasmodium spp., Babesia microti, Babesia divergens, Leishmania tropica, Leishmania spp., Leishmania braziliensis, Leishmania donovani, Trypanosoma gambiense and Trypanosoma rhodesiense (African sleeping sickness), Trypanosoma cruzi (Chagas' disease), and Toxoplasma gondii.

Other medically relevant microorganisms have been described extensively in the literature, e.g., see C. G. A Thomas, Medical Microbiology, Bailliere Tindall, Great Britain 1983, the entire contents of which is hereby incorporated by reference.

As used herein, the terms “cancer antigen” and “tumor antigen” are used interchangeably to refer to antigens which are differentially expressed by cancer cells and can thereby be exploited in order to target cancer cells. Cancer antigens are antigens which can potentially stimulate apparently tumor-specific immune responses. Some of these antigens are encoded, although not necessarily expressed, by normal cells. These antigens can be characterized as those which are normally silent (i.e., not expressed) in normal cells, those that are expressed only at certain stages of differentiation and those that are temporally expressed such as embryonic and fetal antigens. Other cancer antigens are encoded by mutant cellular genes, such as oncogenes (e.g., activated ras oncogene), suppressor genes (e.g., mutant p53), fusion proteins resulting from internal deletions or chromosomal translocations. Still other cancer antigens can be encoded by viral genes such as those carried on RNA and DNA tumor viruses.

The nanostructures of the invention may be delivered to a subject in vivo or ex vivo for therapeutic and/or diagnostic use or may be used in vitro, ex vivo or in vivo for research purposes. Alternatively the nanostructures may be used for the purpose of provoking an immune response for generating reagents such as antibodies or cytokines which can be harvested.

The nanostructures may be administered alone or in any appropriate pharmaceutical carrier, such as a liquid, for example saline, or a powder, for administration in vivo. They can also be co-delivered with larger carrier particles or within administration devices. The nanostructures may be formulated or unformulated. The formulations of the invention can be administered in pharmaceutically acceptable solutions, which may routinely contain pharmaceutically acceptable concentrations of salt, buffering agents, preservatives, compatible carriers, adjuvants, and optionally other therapeutic ingredients. In some embodiments, nanostructures are mixed with a substance such as a lotion (for example, aquaphor) and are administered to the skin of a subject, whereby the nanostructures are delivered through the skin of the subject. It should be appreciated that any method of delivery of nanoparticles known in the art may be compatible with aspects of the invention. The nanostructures may also be sterile.

For use in therapy, an effective amount of the nanostructures can be administered to a subject by any mode that delivers the nanostructures to the desired cell. Administering pharmaceutical compositions may be accomplished by any means known to the skilled artisan. Routes of administration include but are not limited to oral, parenteral, intramuscular, intravenous, subcutaneous, mucosal, intranasal, sublingual, intratracheal, inhalation, ocular, vaginal, dermal, rectal, and by direct injection.

Thus, the invention in one aspect involves the finding that the nanostructures of the invention are highly effective in mediating immune stimulatory effects. These nanostructures (stimulatory and regulatory) are useful therapeutically and prophylactically for modulating the immune system to treat cancer, infectious diseases, allergy, asthma, autoimmune disease, and other disorders and to help protect against opportunistic infections following cancer chemotherapy.

Thus the nanostructures of the invention are useful as a vaccine for the treatment of a subject at risk of developing or a subject having allergy or asthma, an infection with an infectious organism or a cancer in which a specific cancer antigen has been identified. The nanostructures can also be formulated without an antigen or allergen for protection against infection, allergy or cancer, and in this case repeated doses may allow longer term protection. A subject at risk as used herein is a subject who has any risk of exposure to an infection causing pathogen or a cancer or an allergen or a risk of developing cancer. For instance, a subject at risk may be a subject who is planning to travel to an area where a particular type of infectious agent is found or it may be a subject who through lifestyle or medical procedures is exposed to bodily fluids which may contain infectious organisms or directly to the organism or even any subject living in an area where an infectious organism or an allergen has been identified. Subjects at risk of developing infection also include general populations to which a medical agency recommends vaccination with a particular infectious organism antigen. If the antigen is an allergen and the subject develops allergic responses to that particular antigen and the subject may be exposed to the antigen, i.e., during pollen season, then that subject is at risk of exposure to the antigen.

A subject having an infection is a subject that has been exposed to an infectious pathogen and has acute or chronic detectable levels of the pathogen in the body. The nanostructures can be used with or without an antigen to mount an antigen specific systemic or mucosal immune response that is capable of reducing the level of or eradicating the infectious pathogen. An infectious disease, as used herein, is a disease arising from the presence of a foreign microorganism in the body. It is particularly important to develop effective vaccine strategies and treatments to protect the body's mucosal surfaces, which are the primary site of pathogenic entry.

A subject having a cancer is a subject that has detectable cancerous cells. The cancer may be a malignant or non-malignant cancer. Cancers or tumors include but are not limited to biliary tract cancer; brain cancer; breast cancer; cervical cancer; choriocarcinoma; colon cancer; endometrial cancer; esophageal cancer; gastric cancer; intraepithelial neoplasms; lymphomas; liver cancer; lung cancer (e.g. small cell and non-small cell); melanoma; neuroblastomas; oral cancer; ovarian cancer; pancreas cancer; prostate cancer; rectal cancer; sarcomas; skin cancer; testicular cancer; thyroid cancer; and renal cancer, as well as other carcinomas and sarcomas. In one embodiment the cancer is hairy cell leukemia, chronic myelogenous leukemia, cutaneous T-cell leukemia, multiple myeloma, follicular lymphoma, malignant melanoma, squamous cell carcinoma, renal cell carcinoma, prostate carcinoma, bladder cell carcinoma, or colon carcinoma.

A subject shall mean a human or vertebrate animal including but not limited to a dog, cat, horse, cow, pig, sheep, goat, turkey, chicken, primate, e.g., monkey, and fish (aquaculture species), e.g. salmon. Thus, the invention can also be used to treat cancer and tumors, infections, autoimmune disease and allergy/asthma in non-human subjects.

As used herein, the term treat, treated, or treating when used with respect to an disorder such as an infectious disease, autoimmune disease, cancer, allergy, or asthma refers to a prophylactic treatment which increases the resistance of a subject to development of the disease (e.g., to infection with a pathogen) or, in other words, decreases the likelihood that the subject will develop the disease (e.g., become infected with the pathogen) as well as a treatment after the subject has developed the disease in order to fight the disease (e.g., reduce or eliminate the infection) or prevent the disease from becoming worse.

The nanostructures of the invention may also be coated with or administered in conjunction with an anti-microbial agent. An anti-microbial agent, as used herein, refers to a naturally-occurring or synthetic compound which is capable of killing or inhibiting infectious microorganisms. The type of anti-microbial agent useful according to the invention will depend upon the type of microorganism with which the subject is infected or at risk of becoming infected. Anti-microbial agents include but are not limited to anti-bacterial agents, anti-viral agents, anti-fungal agents and anti-parasitic agents. Phrases such as “anti-infective agent”, “anti-bacterial agent”, “anti-viral agent”, “anti-fungal agent”, “anti-parasitic agent” and “parasiticide” have well-established meanings to those of ordinary skill in the art and are defined in standard medical texts. Briefly, anti-bacterial agents kill or inhibit bacteria, and include antibiotics as well as other synthetic or natural compounds having similar functions. Antibiotics are low molecular weight molecules which are produced as secondary metabolites by cells, such as microorganisms. In general, antibiotics interfere with one or more bacterial functions or structures which are specific for the microorganism and which are not present in host cells. Anti-viral agents can be isolated from natural sources or synthesized and are useful for killing or inhibiting viruses. Anti-fungal agents are used to treat superficial fungal infections as well as opportunistic and primary systemic fungal infections. Anti-parasite agents kill or inhibit parasites.

The nanostructures of the invention may also be used for regulating the immune response such that the level of some immune factors are decreased. Achieving specific immune downregulation or “tolerance” is a significant challenge, as the prior art, in general, acts by broadly downregulating immune responses. This non-specific approach can lead to a high incidence of side effects, toxicity, and an increased risk of acquiring infectious diseases, among others. No commercially available compounds or structures have demonstrated the ability to induce potent and specific anti-inflammatory effects in the clinic. A challenge is delivery of the appropriate signals to immune cells, such as antigen, in the absence of additional co-stimulatory signals.

The nanostructures of the invention solve some of these problems encountered by the prior art. In some embodiments an antigen can be delivered intracellularly efficiently via conjugation to a nanostructure of the invention in a manner that achieves or promotes tolerance. The methods may involve antagonizing toll-like receptors during the antigen delivery process in order to enhance the ability to induce antigen-specific tolerance. The nanostructures used for these embodiments of the invention include a liposomal core which is attached to an immune suppressor, such as a TLR 4 immune suppressor and oligonucleotides positioned on the exterior of the core.

These regulatory nanostructures are useful for downregulating an immune response or anytime it is desirable to induce tolerance. For instance, they are useful for treating and preventing autoimmune disease, allergy, asthma, or other conditions where a component of the pathology involves an overactive immune response, such as liver fibrosis or idiopathic pulmonary fibrosis.

A subject having an allergy is a subject that has or is at risk of developing an allergic reaction in response to an allergen. An allergy refers to acquired hypersensitivity to a substance (allergen). Allergic conditions include but are not limited to eczema, allergic rhinitis or coryza, hay fever, conjunctivitis, bronchial asthma, urticaria (hives) and food allergies, and other atopic conditions.

An allergen refers to a substance (antigen) that can induce an allergic or asthmatic response in a susceptible subject. The list of allergens is enormous and can include pollens, insect venoms, animal dander dust, fungal spores and drugs (e.g. penicillin). Examples of natural, animal and plant allergens include but are not limited to proteins specific to the following genuses: Canine (Canis familiaris); Dermatophagoides (e.g. Dermatophagoides farinae); Felis (Felis domesticus); Ambrosia (Ambrosia artemiisfolia; Lolium (e.g. Lolium perenne or Lolium multiflorum); Cryptomeria (Cryptomeria japonica); Alternaria (Alternaria alternata); Alder; Alnus (Alnus gultinoasa); Betula (Betula verrucosa); Quercus (Quercus alba); Olea (Olea europa); Artemisia (Artemisia vulgaris); Plantago (e.g. Plantago lanceolata); Parietaria (e.g. Parietaria officinalis or Parietaria judaica); Blattella (e.g. Blattella germanica); Apis (e.g. Apis multiflorum); Cupressus (e.g. Cupressus sempervirens, Cupressus arizonica and Cupressus macrocarpa); Juniperus (e.g. Juniperus sabinoides, Juniperus virginiana, Juniperus communis and Juniperus ashei); Thuya (e.g. Thuya orientalis); Chamaecyparis (e.g. Chamaecyparis obtusa); Periplaneta (e.g. Periplaneta americana); Agropyron (e.g. Agropyron repens); Secale (e.g. Secale cereale); Triticum (e.g. Triticum aestivum); Dactylis (e.g. Dactylis glomerata); Festuca (e.g. Festuca elatior); Poa (e.g. Poa pratensis or Poa compressa); Avena (e.g. Avena sativa); Holcus (e.g. Holcus lanatus); Anthoxanthum (e.g. Anthoxanthum odoratum); Arrhenatherum (e.g. Arrhenatherum elatius); Agrostis (e.g. Agrostis alba); Phleum (e.g. Phleum pratense); Phalaris (e.g. Phalaris arundinacea); Paspalum (e.g. Paspalum notatum); Sorghum (e.g. Sorghum halepensis); and Bromus (e.g. Bromus inermis).

Autoimmune disease is a class of diseases in which an subject's own antibodies react with host tissue or in which immune effector T cells are autoreactive to endogenous self peptides and cause destruction of tissue. Thus an immune response is mounted against a subject's own antigens, referred to as self antigens. Autoimmune diseases include but are not limited to rheumatoid arthritis, Crohn's disease, multiple sclerosis, systemic lupus erythematosus (SLE), autoimmune encephalomyelitis, myasthenia gravis (MG), Hashimoto's thyroiditis, Goodpasture's syndrome, pemphigus (e.g., pemphigus vulgaris), Grave's disease, autoimmune hemolytic anemia, autoimmune thrombocytopenic purpura, scleroderma with anti-collagen antibodies, mixed connective tissue disease, polymyositis, pernicious anemia, idiopathic Addison's disease, autoimmune-associated infertility, glomerulonephritis (e.g., crescentic glomerulonephritis, proliferative glomerulonephritis), bullous pemphigoid, Sjögren's syndrome, insulin resistance, and autoimmune diabetes mellitus.

A “self-antigen” as used herein refers to an antigen of a normal host tissue. Normal host tissue does not include cancer cells. Thus an immune response mounted against a self-antigen, in the context of an autoimmune disease, is an undesirable immune response and contributes to destruction and damage of normal tissue, whereas an immune response mounted against a cancer antigen is a desirable immune response and contributes to the destruction of the tumor or cancer. Thus, in some aspects of the invention aimed at treating autoimmune disorders it is not recommended that the nanostructure be formulated with self antigens, particularly those that are the targets of the autoimmune disorder.

In other instances, the nanostructures may include small amounts of self-antigens. A number of animal studies have demonstrated that mucosal administration of low doses of antigen can result in a state of immune hyporesponsiveness or “tolerance.” The active mechanism appears to be a cytokine-mediated immune deviation away from a Th1 towards a predominantly Th2 and Th3 (i.e., TGF-β dominated) response. The active suppression with low dose antigen delivery can also suppress an unrelated immune response (bystander suppression) which is of considerable interest in the therapy of autoimmune diseases, for example, rheumatoid arthritis and SLE. Bystander suppression involves the secretion of Th1-counter-regulatory, suppressor cytokines in the local environment where proinflammatory and Th1 cytokines are released in either an antigen-specific or antigen-nonspecific manner. “Tolerance” as used herein is used to refer to this phenomenon. Indeed, oral tolerance has been effective in the treatment of a number of autoimmune diseases in animals including: experimental autoimmune encephalomyelitis (EAE), experimental autoimmune myasthenia gravis, collagen-induced arthritis (CIA), and insulin-dependent diabetes mellitus. In these models, the prevention and suppression of autoimmune disease is associated with a shift in antigen-specific humoral and cellular responses from a Th1 to Th2/Th3 response.

In another aspect, the present invention is directed to a kit including one or more of the compositions previously discussed. A “kit,” as used herein, typically defines a package or an assembly including one or more of the compositions of the invention, and/or other compositions associated with the invention, for example, as previously described. Each of the compositions of the kit, if present, may be provided in liquid form (e.g., in solution), or in solid form (e.g., a dried powder). In certain cases, some of the compositions may be constitutable or otherwise processable (e.g., to an active form), for example, by the addition of a suitable solvent or other species, which may or may not be provided with the kit. Examples of other compositions that may be associated with the invention include, but are not limited to, solvents, surfactants, diluents, salts, buffers, emulsifiers, chelating agents, fillers, antioxidants, binding agents, bulking agents, preservatives, drying agents, antimicrobials, needles, syringes, packaging materials, tubes, bottles, flasks, beakers, dishes, frits, filters, rings, clamps, wraps, patches, containers, tapes, adhesives, and the like, for example, for using, administering, modifying, assembling, storing, packaging, preparing, mixing, diluting, and/or preserving the compositions components for a particular use, for example, to a sample and/or a subject.

In some embodiments, a kit associated with the invention includes one or more components of the nanostructure. For instance the kit may include liposomes for forming a liposome core, an immune stimulant or TLR4 immune suppressor and or oligonucleotides for the exterior of the nanostructure. A kit can also include one or more antigens and or other therapeutic agents.

A kit of the invention may, in some cases, include instructions in any form that are provided in connection with the compositions of the invention in such a manner that one of ordinary skill in the art would recognize that the instructions are to be associated with the compositions of the invention. For instance, the instructions may include instructions for the use, modification, mixing, diluting, preserving, administering, assembly, storage, packaging, and/or preparation of the compositions and/or other compositions associated with the kit. In some cases, the instructions may also include instructions for the use of the compositions, for example, for a particular use, e.g., to a sample. The instructions may be provided in any form recognizable by one of ordinary skill in the art as a suitable vehicle for containing such instructions, for example, written or published, verbal, audible (e.g., telephonic), digital, optical, visual (e.g., videotape, DVD, etc.) or electronic communications (including Internet or web-based communications), provided in any manner.

EXAMPLES

In order that the invention described herein may be more fully understood, the following examples are set forth. The examples described in this application are offered to illustrate the compounds, pharmaceutical compositions, and methods provided herein and are not to be construed in any way as limiting their scope.

Example 1

In one embodiment reduced to practice, oligonucleotides of sequence 5′-TCCATGACGTTCCTGACGTT-3′ (SEQ ID NO:1; designated as “CpG 1826”) were 3′-modified with alpha-tocopherol and incorporated into small unilamellar vesicles composed of (92% w/w) 1,2-dioleoyl-sn-glycero-3-phosphatidylcholine (DOPC) mixed with (8% w/w) monophosphoryl lipid A (FIG. 1). In a sub-embodiment, these structures were further conjugated with ovalbumin, a model protein antigen via Watson-Crick type hybridization of an ovalbumin-oligo construct, where the oligo portion was complementary to CpG 1826 (5′-AACGTCAGGAACGTCATGGA-3′ SEQ ID NO:2) (FIG. 2). The oligonucleotide here was selected on the basis of its ability to stimulate TLR9, whereas MPLA was selected for its ability to stimulate TLR4.

Liposomal SNA (Nanostructure) Synthesis

25 mg of 1,2-dioleoyl-sn-glycero-3-phosphatidylcholine (DOPC) dissolved in 4 mL dichloromethane (DCM) was mixed with 1 mg monophosphoryl lipid A (MPLA) dissolved in 1 mL of chloroform in a glass container. The lipids were then dried onto the walls of the glass container in a thin film by gently drying under argon until all solvent has evaporated. Any residual solvent was removed by overnight lyophilization. The next day, the lipids were reconstituted in 10 mL of liposome buffer (150 mM NaCl, 20 mM HEPES) by vortex and sonication, then passed through 2-5 freeze thaw cycles prior to serial extrusion through 100 nm, 50 nm, then 30 nm extrusion membranes. Following extrusion, 1 umol of oligonucleotide (5′-TCCATGACGTTCCTGACGTT-3′ SEQ ID NO:1) with a 3′-alpha-tocopherol group covalently attached) was mixed with the 26 mg of lipid and incubated overnight at 4 C to form the liposomal SNAs. The following day, the liposomal SNAs were purified by tangential flow filtration using a 300 kDa membrane cutoff filter using >5 volume exchanges of 1×PBS.

Some liposomal SNAs were additionally modified to contain ovalbumin by conjugating the ovalbumin first to an oligonucleotide complementary to CpG 1826 (5′-AACGTCAGGAACGTCATGGA-3′ SEQ ID NO:2). This ovalbumin-oligonucleotide conjugate was then hybridized to the liposomal SNAs by incubating at a 2-fold excess of ovalbumin-oligonucleotide conjugate relative to oligonucleotide on the liposomal SNA for 3 hours at 37 C, followed by overnight incubation at 4 C. Excess ovalbumin-oligonucleotide conjugate was removed by tangential flow filtration.

In Vitro Testing

The compounds were serially diluted 1:4. 20 uL of this mixture was seeded in duplicate in a 96 well plate. RAW Blue cells (InVivoGen), a reporter murine macrophage cell line derived from RAW 264.7 cells containing a NF-kB inducible secreted alkaline phosphatase (SEAP) were seeded at 100 k cells/well in 180 uL per well and added to the test compounds on the 96 well plate. Ramos Blue cells (InvivoGen), a reporter human B cell line derived from Ramos cells containing a NF-kB inducible SEAP were seeded at 306 k cells/well in 180 uL per well and added to the test compounds on the 96 well plate. Importantly, Ramos Blue cells do not have functional signaling through TLR4. The cells were incubated with the test compound overnight at 37 C, 5% CO2 in a humidified chamber. The following day, the supernatants were probed for SEAP activity using the QuantiBlue reagent (InVivoGen) following the manufacturer recommended protocol. The results show that liposomal SNAs which carry agonists of both TLR4 and TLR9 induce greater activation of the RAW Blue cells that either alone in isolation (FIG. 4). Importantly, the results show that activation of NF-kB by liposomal SNAs containing MPLA depended on functional TLR4, as the RAW Blue cell line but not the Ramos Blue cell line demonstrated NF-kB activation in response to stimulation (FIG. 5).

To further profile the response triggered by liposomal SNAs containing both TLR9 and TLR4 agonists, the ability of liposomal SNAs to induce activation of MyD88-dependent and MyD88-independent pathways was tested, as measured by activation levels of TNF and IFN-alpha, respectively. For this, 6 million human peripheral blood mononuclear cells (PBMCs) were resuspended at 1 million/mL in RPMI-1640 supplemented with 10% FBS and 1% penicillin/streptomycin and seeded at 180 k/well with 20 uL of test compound. Following overnight incubation, the supernatant was probed for TNF and IFN-alpha levels by ELISA. The results show that liposomal SNAs that deliver both CpG 1826 and MPLA in a single construct demonstrate elevated TNF and IFN-alpha levels that cannot be replicated either by delivering each in isolation, or by delivering both components in the same well but not on the same construct (FIG. 6). Even when a sequence that did not activate TLR9 (designated as “CTL-ps”: 5′-TCCATGAGCTTCCTGAGCTT-3′ SEQ ID NO:3) was used to construct the liposomal SNA, enhanced activity of MPLA was observed (FIG. 7), suggesting that the liposomal SNA delivers MPLA more efficiently than a liposomal formulation.

Next, parameters that might modulate the efficacy of the liposomal SNAs were identified. The quantity of MPLA feed into the liposomal formulation step might play a role, as well as the internucleotide linkage chemistry (PO vs PS). Accordingly, liposomal SNAs were developed with increasing MPLA feed from 3.8% (w/w) to 11.5% (w/w) and constructs containing both PO and PS linkages and tested them for activity in RAW Blue cells. In this cell line, it was observed that increasing the MPLA feed up to 7.7% MPLA but not up to 11.5% increased the potency of activation of the liposomal SNA (FIG. 8). In the RAW Blue cells, a shift was observed in the potency of the liposomal SNA but not in the maximal stimulation (FIG. 9), though this is anticipated to be species dependent.

Finally, the ability of antigen-conjugated liposomal SNAs to activate immune cells was tested. Ovalbumin loaded liposomal SNAs were incubated as described with RAW Blue cells overnight at the level of SEAP probed by QuantiBlue assay. Conjugation of antigen to the liposomal SNAs appeared to increase their activity (FIG. 10). It is possible that this occurs due to the presence of additional CpG motifs introduced by the complementary oligonucleotide that is attached to the ovalbumin, which formed duplexes with CpG 1826.

In Vivo Testing

This form of antigen delivery has been shown to induce more potent induction of immune stimulatory effects in vitro (FIG. 10) and induce effective antigen processing and presentation, leading to effective induction of an anti-tumor immune response in vivo (FIGS. 11-12).

C57BL/6 mice (N=4/group) were immunized (200 μL s.c., 100 μg ovalbumin equivalent dose) with the indicated formulations on day 0 and 21 using ovalbumin as the model antigen (FIG. 11). On day 28, splenocytes were collected and incubated overnight on IFN-y ELISPOT plates with 1 uM OVA(257-264). The number of IFN-y spots was quantified using an automated ELISPOT counter. This study shows that SNAs induce cellular responses more effectively than free PS oligo and alum. *p<0.05, NS=non-significant.

In another experiment, C57BL/6 mice (N=11/group) were inoculated with 1×10⁶ E.G7-OVA cells (ATCC #CRL-2113) on day 0 then treated with the indicated compounds on days 3, 7, 10 (200 μL s.c., 100 μg ovalbumin equivalent dose). Tumor volume was calculated by measuring the length and width of the subcutaneous tumor and applying the formula tumor volume=(length)×(width)×(width)/2. The results demonstrate activation of strong cellular responses to antigen in vivo with evidence of significant (95%) reduction of tumor burden (FIG. 12).

In the claims articles such as “a,” “an,” and “the” may mean one or more than one unless indicated to the contrary or otherwise evident from the context. Claims or descriptions that include “or” between one or more members of a group are considered satisfied if one, more than one, or all of the group members are present in, employed in, or otherwise relevant to a given product or process unless indicated to the contrary or otherwise evident from the context. The invention includes embodiments in which exactly one member of the group is present in, employed in, or otherwise relevant to a given product or process. The invention includes embodiments in which more than one or all of the group members are present in, employed in or otherwise relevant to a given product or process.

Furthermore, the invention encompasses all variations, combinations, and permutations in which one or more limitations, elements, clauses, and descriptive terms from one or more of the listed claims is introduced into another claim. For example, any claim that is dependent on another claim can be modified to include one or more limitations found in any other claim that is dependent on the same base claim. Where elements are presented as lists, e.g., in Markush group format, each subgroup of the elements is also disclosed, and any element(s) can be removed from the group. It should it be understood that, in general, where the invention, or aspects of the invention, is/are referred to as comprising particular elements and/or features, certain embodiments of the invention or aspects of the invention consist, or consist essentially of, such elements and/or features. For purposes of simplicity, those embodiments have not been specifically set forth in haec verba herein. It is also noted that the terms “comprising” and “containing” are intended to be open and permits the inclusion of additional elements or steps. Where ranges are given, endpoints are included. Furthermore, unless otherwise indicated or otherwise evident from the context and understanding of one of ordinary skill in the art, values that are expressed as ranges can assume any specific value or sub-range within the stated ranges in different embodiments of the invention, to the tenth of the unit of the lower limit of the range, unless the context clearly dictates otherwise.

This application refers to various issued patents, published patent applications, journal articles, and other publications, all of which are incorporated herein by reference. If there is a conflict between any of the incorporated references and the instant specification, the specification shall control. In addition, any particular embodiment of the present invention that falls within the prior art may be explicitly excluded from any one or more of the claims. Because such embodiments are deemed to be known to one of ordinary skill in the art, they may be excluded even if the exclusion is not set forth explicitly herein. Any particular embodiment of the invention can be excluded from any claim, for any reason, whether or not related to the existence of prior art.

Those skilled in the art will recognize or be able to ascertain using no more than routine experimentation many equivalents to the specific embodiments described herein. The scope of the present embodiments described herein is not intended to be limited to the above Description, but rather is as set forth in the appended claims. Those of ordinary skill in the art will appreciate that various changes and modifications to this description may be made without departing from the spirit or scope of the present invention, as defined in the following claims. 

We claim:
 1. A nanostructure, comprising a liposomal core having a lipid bilayer, wherein a nucleic acid immune stimulant that stimulates toll like receptors is associated with the lipid bilayer, and oligonucleotides positioned on the exterior of the liposomal core in the form of an oligonucleotide shell, wherein the oligonucleotides comprise CpG-motif containing oligonucleotides and the CpG-motif containing oligonucleotides are B-class CpG oligonucleotides, wherein the oligonucleotides are indirectly linked to the liposomal core through a linker, wherein all of the oligonucleotides have their 5′-termini exposed to the outside surface of the nanostructure, and wherein the linker is cholesterol.
 2. The nanostructure of claim 1, wherein the nanostructure comprises at least 25 oligonucleotides in the shell.
 3. The nanostructure of claim 1, wherein the oligonucleotides are oriented radially outwards from the liposomal core.
 4. The nanostructure of claim 1, wherein the liposomal core is comprised of phospholipids.
 5. The nanostructure of claim 4, wherein the phospholipids are phosphatidylcholines.
 6. The nanostructure of claim 1, wherein the nanostructure is a self-assembling nanostructure.
 7. A composition for use in the treatment of disease, comprising the nanostructure of claim
 1. 8. The nanostructure of claim 1, wherein the oligonucleotide shell is comprised entirely of oligonucleotides.
 9. The nanostructure of claim 1, wherein the oligonucleotides of the oligonucleotide shell have structurally identical oligonucleotides.
 10. The nanostructure of claim 1, wherein the oligonucleotides have at least one phosphorothioate linkage. 